SSU rRNA sequencing data for bacterial communities of the mucosa and the gut contents of rainbow trout (Oncorhynchus mykiss) on a high-carbohydrate and high-protein diet

The growing aquaculture industry requires more feed resources and the development of alternative feed formulations to replace costly fishmeal. Given the markedly large observed variability in the composition of the gut microbiota among fish populations, it is assumed that diet can significantly influence the bacterial communities of salmonids. This effect should be taken into account because intestine microbiota is known to be essential not only for the effective assimilation of food, but also for the functioning of the immune system of the fish. The data presented relate to the possibility of changing the intestinal microbiome of carnivorous fish rainbow trout Oncorhynchus mykiss fed with an extremely high-carbohydrate diet in comparison with a high-protein diet based on fishmeal. Total DNA was isolated from these samples and used to produce v3-v4 SSU rRNA amplicons, which were then sequenced on Illumina MiSeq (2 × 300 bp) and assembled into 97% identity OTUs. The dataset provides information on the bacterial communities of the parietal microflora (autochthonous) of the rainbow trout intestine, as well as the composition of the chyme microbiota (allochthonous) depending on the fish diet.